Alternatively, if the map is only for single-player, you can use combat scripts.
Another trick you can try is to replace the standard action when attacking a neutral unit and force the hero to fight another army (using StartCombat, where you can specify all the units to fight in detail). After the battle, if victorious, delete the neutral unit with a script, which we "attacked." In case of defeat, it will be more complicated – combat scripts will be needed again to check how many enemies we managed to kill before the defeat, in order to subtract them from the neutral army. Or you can ignore this moment and do nothing in case of defeat.
Obviously, the simplest option is the first one.